def load_all_cached_profile_data(meta_dir: Path,
glob_pattern: typing.Union[Path, str]):
glob_pattern = str(glob_pattern)
return xr.concat(
(pio.load_profile_data(p)
for p in sorted(meta_dir.glob(glob_pattern))),
dim="animal",
)
def test_standardization(self, matlab_engine, shared_datadir):
raw_data = pio.load_profile_data(
shared_datadir / "experiments" / "2017_02_23-HD233_HD236" /
"analyses" / "2020-05-22" /
"2017_02_23-HD233_HD236-untrimmed_profile_data.nc").isel(
animal=[0, 1, 2])
std_data, std_warp = pp.standardize_profiles(
raw_data,
redox_params=self.redox_params,
eng=matlab_engine,
**self.reg_d2_parameters,
)
assert raw_data.animal.size == std_data.animal.size
def test_channel_registration(self, matlab_engine, shared_datadir):
raw_data = pio.load_profile_data(
shared_datadir / "experiments" / "2017_02_23-HD233_HD236" /
"analyses" / "2020-05-22" /
"2017_02_23-HD233_HD236-untrimmed_profile_data.nc").isel(
animal=[0, 1, 2])
reg_data, warp_data = pp.channel_register(
raw_data,
redox_params=self.redox_params,
eng=matlab_engine,
reg_params=self.reg_d2_parameters,
)
assert raw_data.animal.size == reg_data.animal.size
def load_masks(self):
self.seg_images = pio.load_profile_data(self.seg_images_path)
logging.info(f"Loaded masks from {self.seg_images_path}")
from pharedox import pio as pio
from pharedox import plots
from pharedox import profile_processing as pp
from pharedox import utils
logging.basicConfig(
format="%(asctime)s %(levelname)s:%(message)s",
level=logging.DEBUG,
datefmt="%I:%M:%S",
)
meta_dir = Path("/Users/sean/code/pharedox/data/paired_ratio")
prof_raw = xr.concat(
[
pio.load_profile_data(x) for x in sorted(
meta_dir.glob("**/2020-01-09_unregistered/*untrimmed*.nc"))
],
dim="animal",
)
prof_raw = prof_raw.assign_coords(
{"position": np.linspace(0, 1, prof_raw.position.size)})
rot_fl = xr.load_dataarray(
"/Users/sean/code/pharedox/data/paired_ratio/all_rot_fl.nc").rename(
{"spec": "animal"})
rot_seg = xr.load_dataarray(
"/Users/sean/code/pharedox/data/paired_ratio/all_rot_seg.nc").rename(
{"spec": "animal"})
midlines = ip.calculate_midlines(rot_seg)